and then she puts your hand on her stomach signifying she's pregnant, and the game ends.

What the hell man? Lol. You were preparing for some epic battle and it's like "RAPE RAPE RAPE! BABY!"

I guess being a Father is PRETTY scary though.

Oddly enough though, the rape scene was pretty sexeh for a game like F.E.A.R. Alma looked like she was Asian-ish and pretty much naked.(Talking about her healthy adult form...not the skinny I've been in water my whole life form)

Lots about the game left though. Music box, tree, teddy bear. So much left unexplored, probably for the third? How long do they want to drag this out? It's an interesting way to go with the series, but I thought a two-parter would round it off well.

I loled so hard in the earlier scene, when you go into the facility and Alma runs and and full on Glomps you.
I was like "She glomped me...she...Oh. That's why she's chasing me..."

Also, a point to consider, the point of a 'silent protagonist' is to better immerse the player into the character, to give the impression that he thinks what you think, and just never happens to say anything. Basically character=you.
Second point, its not rape if you want it.

In my mind, Beckett and Alma will now happily raise a family on the island, occasionally slaughtering anyone who trespasses.

To get the 'good' end, you have to get all the reflex boosters, then beat the game. This unlocks a golden booster in the first level that replaces your melee attack with a psychic blast. It starts off pretty weak, but gets stronger at different plot points.

If you go through the whole game using only the psychic blast, you unlock the 'good' end.